Faraz Hach

25 papers B 2C 2Journal 21
YearRankTypeTitle / Venue / Authors
2024 J jnl
TKSM: highly modular, user-customizable, and scalable transcriptomic sequencing long-read simulator.
Bioinform.
Fatih Karaoglanoglu, Baraa Orabi, Ryan Flannigan, Cédric Chauve, Faraz Hach
2022 J jnl
Fast characterization of segmental duplication structure in multiple genome assemblies.
Algorithms Mol. Biol.
Hamza Iseric, Can Alkan, Faraz Hach, Ibrahim Numanagic
2021 C conf
BISER: Fast Characterization of Segmental Duplication Structure in Multiple Genome Assemblies.
WABI
Hamza Iseric, Can Alkan, Faraz Hach, Ibrahim Numanagic
2021 J jnl
Detecting high-scoring local alignments in pangenome graphs.
Bioinform.
Tizian Schulz, Roland Wittler, Sven Rahmann, Faraz Hach, Jens Stoye
2020 J jnl
CircMiner: accurate and rapid detection of circular RNA through splice-aware pseudo-alignment scheme.
Bioinform.
Hossein Asghari, Yen-Yi Lin, Yang Xu, Ehsan Haghshenas, Colin C. Collins, Faraz Hach
2019 J jnl
Alignment-free clustering of UMI tagged DNA molecules.
Bioinform.
Baraa Orabi, Emre Erhan, Brian McConeghy, Stanislav V. Volik, Stephane Le Bihan, Robert Bell, Colin C. Collins, Cédric Chauve, Faraz Hach
2019 J jnl
lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data.
Bioinform.
Ehsan Haghshenas, Süleyman Cenk Sahinalp, Faraz Hach
2018 J jnl
Computational identification of micro-structural variations and their proteogenomic consequences in cancer.
Bioinform.
Yen-Yi Lin, Alexander Gawronski, Faraz Hach, Sujun Li, Ibrahim Numanagic, Iman Sarrafi, Swati Mishra, Andrew W. McPherson, Colin C. Collins, Milan Radovich, Haixu Tang, Süleyman Cenk Sahinalp
2018 J jnl
Dynamic Alignment-Free and Reference-Free Read Compression.
J. Comput. Biol.
Guillaume Holley, Roland Wittler, Jens Stoye, Faraz Hach
2018 J jnl
Fast Characterization of Segmental Duplications in Genome Assemblies.
CoRR
Ibrahim Numanagic, Alim S. Gökkaya, Lillian Zhang, Bonnie Berger, Can Alkan, Faraz Hach
2018 J jnl
Fast characterization of segmental duplications in genome assemblies.
Bioinform.
Ibrahim Numanagic, Alim S. Gökkaya, Lillian Zhang, Bonnie Berger, Can Alkan, Faraz Hach
2017 J jnl
Discovery and genotyping of novel sequence insertions in many sequenced individuals.
Bioinform.
Pinar Kavak, Yen-Yi Lin, Ibrahim Numanagic, Hossein Asghari, Tunga Güngör, Can Alkan, Faraz Hach
2017 B conf
Dynamic Alignment-Free and Reference-Free Read Compression.
RECOMB
Guillaume Holley, Roland Wittler, Jens Stoye, Faraz Hach
2017 J jnl
SiNVICT: ultra-sensitive detection of single nucleotide variants and indels in circulating tumour DNA.
Bioinform.
Can Kockan, Faraz Hach, Iman Sarrafi, Robert H. Bell, Brian McConeghy, Kevin Beja, Anne Haegert, Alexander W. Wyatt, Stanislav Volik, Kim N. Chi, Colin C. Collins, Süleyman Cenk Sahinalp
2016 J jnl
CoLoRMap: Correcting Long Reads by Mapping short reads.
Bioinform.
Ehsan Haghshenas, Faraz Hach, Süleyman Cenk Sahinalp, Cédric Chauve
2014 J jnl
ORMAN: Optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms.
Bioinform.
Phuong Dao, Ibrahim Numanagic, Yen-Yi Lin, Faraz Hach, Emre Karakoç, Nilgun Donmez, Colin C. Collins, Evan E. Eichler, Süleyman Cenk Sahinalp
2014 J jnl
mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications.
Nucleic Acids Res.
Faraz Hach, Iman Sarrafi, Farhad Hormozdiari, Can Alkan, Evan E. Eichler, Süleyman Cenk Sahinalp
2012 C conf
CLIIQ: Accurate Comparative Detection and Quantification of Expressed Isoforms in a Population.
WABI
Yen-Yi Lin, Phuong Dao, Faraz Hach, Marzieh Bakhshi, Fan Mo, Anna Lapuk, Colin C. Collins, Süleyman Cenk Sahinalp
2012 J jnl
Dissect: detection and characterization of novel structural alterations in transcribed sequences.
Bioinform.
Deniz Yörükoglu, Faraz Hach, Lucas Swanson, Colin C. Collins, Inanç Birol, Süleyman Cenk Sahinalp
2012 J jnl
SCALCE: boosting sequence compression algorithms using locally consistent encoding.
Bioinform.
Faraz Hach, Ibrahim Numanagic, Can Alkan, Süleyman Cenk Sahinalp
2012 J jnl
Sensitive and fast mapping of di-base encoded reads.
Bioinform.
Farhad Hormozdiari, Faraz Hach, Süleyman Cenk Sahinalp, Evan E. Eichler, Can Alkan
2011 J jnl
Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data.
Bioinform.
Andrew W. McPherson, Chunxiao Wu, Iman Hajirasouliha, Fereydoun Hormozdiari, Faraz Hach, Anna Lapuk, Stanislav Volik, Sohrab P. Shah, Colin C. Collins, Süleyman Cenk Sahinalp
2011 J jnl
Sensitive and fast mapping of di-base encoded reads.
Bioinform.
Farhad Hormozdiari, Faraz Hach, Süleyman Cenk Sahinalp, Evan E. Eichler, Can Alkan
2010 J jnl
Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery.
Bioinform.
Fereydoun Hormozdiari, Iman Hajirasouliha, Phuong Dao, Faraz Hach, Deniz Yörükoglu, Can Alkan, Evan E. Eichler, Süleyman Cenk Sahinalp
2007 B conf
Faster Phylogenetic Inference with MXG.
LPAR
David G. Mitchell, Faraz Hach, Raheleh Mohebali